You're right; unfixed films are still light sensitive but after the developer has been neutralized by the acid stop bath image formation is suspended -- for a while. Films (and especially papers) will darken from the effects of light exposure alone but it's a slow process. Practically, if you have treated developed films in a standard acid stop bath for a minute or two, with agitation, you should be able to extract the sheets from the tubes and load them onto your Jobo reels safely in dim room light. Obviously you shouldn't prolong the exposure more than necessary, but there's no need to panic, either.
Note that there are some developers, such as Amidol, that are active in an acid solution, so this procedure isn't safe for them. But I don't think you'll be at risk with any of the popular film developers.